Opened 21 months ago
Closed 18 months ago
#14510 closed defect (fixed)
KeyError restoring tasks
Reported by: | Owned by: | Zach Pearson | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Sessions | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.19045 ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open "D:\Promotion\002_Material\Proteine, > PDB\ChimeraX\hDicer_ChimeraX\hDicer_5zak_viridis_categorical_named.cxs" > format session Log from Wed Jan 31 14:53:35 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open "D:\Promotion\002_Material\Proteine, > PDB\ChimeraX\hDicer_ChimeraX\hDicer_5zak_viridis_categorical.cxs" format > session Log from Wed Jan 31 14:23:59 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open "D:\Promotion\002_Material\Proteine, > PDB\ChimeraX\hDicer_ChimeraX\hDicer_5zak_viridis_categorical.cxs" format > session Log from Wed Jan 31 14:05:13 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open "D:\Promotion\002_Material\Proteine, > PDB\ChimeraX\Dicer_5zak_viridis_catagorical.cxs" format session Log from Wed Jan 31 12:50:37 2024UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open "D:\Promotion\002_Material\Proteine, > PDB\ChimeraX\Dicer_5zak_viridis_catagorical.cxs" format session Log from Wed Jan 31 12:12:08 2024 Startup Messages --- warning | Your computer has Intel graphics driver 6793 with a known bug that causes all Qt user interface panels to be blank. ChimeraX can partially fix this but may make some panel titlebars and edges black. Hopefully newer Intel graphics drivers will fix this. You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Updating list of available bundles failed: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1129) > open "D:/Promotion/002_Material/Proteine, PDB/Chimera Sessions and > Images/hDicer_PNG from PDB/hDicer_labelled domains/hDicer_5ZAK_labelled > domains_viridis_categorical_Viewing.py" ChimeraX cannot open a regular Chimera session. An exporter from Chimera to ChimeraX is being worked on but only handles molecules and molecular surfaces (not volumes) at this time. If that is sufficient, use the latest Chimera daily build and its File->Export Scene menu item, and change the resulting dialog's "File Type" to ChimeraX. > open "D:/Promotion/002_Material/Proteine, PDB/Chimera Sessions and > Images/hDicer_PNG from PDB/hDicer_labelled domains/hDicer_5ZAK_labelled > domains_viridis_categorical_Viewing.pyc" Python code was compiled for a different version of Python > open "D:/Promotion/002_Material/Proteine, PDB/Chimera Sessions and > Images/hDicer_PNG from PDB/hDicer_labelled domains/hDicer_5ZAK_labelled > domains_viridis_categorical.py" ChimeraX cannot open a regular Chimera session. An exporter from Chimera to ChimeraX is being worked on but only handles molecules and molecular surfaces (not volumes) at this time. If that is sufficient, use the latest Chimera daily build and its File->Export Scene menu item, and change the resulting dialog's "File Type" to ChimeraX. > open "D:/Promotion/002_Material/Proteine, PDB/Chimera Sessions and > Images/hDicer_PNG from PDB/hDicer_labelled domains/hDicer_5ZAK_labelled > domains_HMmod.pyc" Python code was compiled for a different version of Python > open "D:\Promotion\002_Material\Proteine, PDB\PDB files\hDicer_PDB > files\hDicer_AF-Q9UPY3-F1-model_v1_AlphaFold_Dicer.pdb" format pdb hDicer_AF-Q9UPY3-F1-model_v1_AlphaFold_Dicer.pdb title: Alphafold V2.0 prediction for endoribonuclease dicer (Q9UPY3) [more info...] Chain information for hDicer_AF-Q9UPY3-F1-model_v1_AlphaFold_Dicer.pdb #1 --- Chain | Description | UniProt A | endoribonuclease dicer | DICER_HUMAN > open C:\Users\Henri\Downloads\ChimeraX\AlphaFold\prediction_1\best_model.pdb > format pdb Chain information for best_model.pdb #2 --- Chain | Description B | No description available C | No description available > open C:\Users\Henri\Downloads\ChimeraX\AlphaFold\prediction_2\best_model.pdb > format pdb Chain information for best_model.pdb #3 --- Chain | Description B | No description available C | No description available > open pdb:5zak Summary of feedback from opening 5zak fetched from pdb --- note | Fetching compressed mmCIF 5zak from http://files.rcsb.org/download/5zak.cif 5zak title: Cryo-EM structure of human Dicer and its complexes with a pre-miRNA substrate [more info...] Chain information for 5zak #4 --- Chain | Description | UniProt A | Endoribonuclease Dicer | DICER_HUMAN B | RISC-loading complex subunit TARBP2 | TRBP2_HUMAN > open pdb:5zak format mmcif fromDatabase pdb 5zak title: Cryo-EM structure of human Dicer and its complexes with a pre-miRNA substrate [more info...] Chain information for 5zak #5 --- Chain | Description | UniProt A | Endoribonuclease Dicer | DICER_HUMAN B | RISC-loading complex subunit TARBP2 | TRBP2_HUMAN > select add #1 15365 atoms, 15708 bonds, 1922 residues, 1 model selected > select add #2 17418 atoms, 17812 bonds, 2172 residues, 2 models selected > select add #3 22480 atoms, 22999 bonds, 2807 residues, 3 models selected > hide #3 target m > show #3 models > hide #3 target m > hide #2 target m > hide #1 target m > close #1 > close #2 > close #3 > set bgColor white > open pdb:5zak format mmcif fromDatabase pdb 5zak title: Cryo-EM structure of human Dicer and its complexes with a pre-miRNA substrate [more info...] Chain information for 5zak #1 --- Chain | Description | UniProt A | Endoribonuclease Dicer | DICER_HUMAN B | RISC-loading complex subunit TARBP2 | TRBP2_HUMAN > open pdb:5zak format mmcif fromDatabase pdb 5zak title: Cryo-EM structure of human Dicer and its complexes with a pre-miRNA substrate [more info...] Chain information for 5zak #2 --- Chain | Description | UniProt A | Endoribonuclease Dicer | DICER_HUMAN B | RISC-loading complex subunit TARBP2 | TRBP2_HUMAN > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!5 models > show #!5 models > show #!1 models > hide #!4 models > hide #!5 models > hide #!1 models > show #!1 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > close #2 > close #4 > close #5 > save "D:/Promotion/002_Material/Proteine, > PDB/ChimeraX/Dicer_5zak_viridis_catagorical.cxs" ——— End of log from Wed Jan 31 12:12:08 2024 ——— opened ChimeraX session > save "D:/Promotion/002_Material/Proteine, > PDB/ChimeraX/Dicer_5zak_viridis_catagorical.cxs" ——— End of log from Wed Jan 31 12:50:37 2024 ——— opened ChimeraX session > colour yellow @1-565 > color yellow @1-565 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color yellow @1-565 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color yellow @1-565 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > ui tool show Updates > ui tool show "Color Actions" > ui tool show "Blast Protein" > ui tool show "Show Sequence Viewer" > sequence chain /A Alignment identifier is 1/A > select clear > select /A:45-556 3686 atoms, 3749 bonds, 2 pseudobonds, 459 residues, 2 models selected > color sel blue > color (#!1 & sel) #ee99eeff > color (#!1 & sel) #e9e936ff > select /A:565 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:45-565 3757 atoms, 3821 bonds, 2 pseudobonds, 468 residues, 2 models selected > color #454581 @566-590 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color blue @566-590 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color blue residues @566-590 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color rsidues 566 to 590 in blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/A:1-565 #454581 > color #1/B:1-565 #05BFEB > blastprotein /B database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version > None name bp1 Webservices job id: LJS748IKUBNBV6Q6 > color #1/A:1-565 #e9e936 > color #1/A:566-590 #454581 > color #1/A:591-715 #969687 > color #1/A:716-752 #58588e > color #1/A:753-903 #cbcb4a > color #1/A:904-1042 #7f7f90 > color #1/A:1043-1078 #bcbc5f > color #1/A:1079-1293 #737391 > color #1/A:1294-1633 #aeae70 > color #1/A:1634-1850 #3a3a5f > color #1/A:1851-1922 #e73952 > save "D:/Promotion/002_Material/Proteine, > PDB/ChimeraX/hDicer_ChimeraX/hDicer_5zak_viridis_categorical.cxs" [Repeated 1 time(s)] ——— End of log from Wed Jan 31 14:05:13 2024 ——— opened ChimeraX session BLAST job failed > select #1/A:479 8 atoms, 7 bonds, 1 residue, 1 model selected > label sel residues text Helicase color #e9e936 height 44 > select #1/A:479 8 atoms, 7 bonds, 1 residue, 1 model selected > label sel residues text Helicase color #e9e936 height 4 > select #1/A:479 8 atoms, 7 bonds, 1 residue, 1 model selected > label sel residues text Helicase color #e9e936 height 8 > ui tool show "Show Sequence Viewer" > select /B 560 atoms, 566 bonds, 75 residues, 1 model selected > select clear > select #1/A:570 9 atoms, 8 bonds, 1 residue, 1 model selected > label sel residues text Pincer-like color #454581 depth 8 Expected a keyword > save "D:/Promotion/002_Material/Proteine, > PDB/ChimeraX/hDicer_ChimeraX/hDicer_5zak_viridis_categorical.cxs" ——— End of log from Wed Jan 31 14:23:59 2024 ——— opened ChimeraX session BLAST job failed > select #1/A:568 9 atoms, 8 bonds, 1 residue, 1 model selected > label sel residues text Pincer-like color #454581 height 8 > select #1/A:568 9 atoms, 8 bonds, 1 residue, 1 model selected > label sel residues text Pincer-like color #454581 height 1 > select #1/A:568 9 atoms, 8 bonds, 1 residue, 1 model selected > label sel residues text Pincer-like color #454581 height 8 > select #1/A:570 9 atoms, 8 bonds, 1 residue, 1 model selected > label sel residues text Pincer-like color #454581 height 8 > select #1/A:570 9 atoms, 8 bonds, 1 residue, 1 model selected > label sel residues text Pincer-like color #454581 height 0 > select #1/A:568 9 atoms, 8 bonds, 1 residue, 1 model selected > label sel residues text Pincer-like color #454581 height 0 > select #1/A:569 8 atoms, 7 bonds, 1 residue, 1 model selected > label sel residues text Pincer-like color #454581 height 8 > select #1/B:299 6 atoms, 5 bonds, 1 residue, 1 model selected > label sel residues text TRBP color #e9e936 height 8 > select #1/B:299 6 atoms, 5 bonds, 1 residue, 1 model selected > label sel residues text TRBP color #05bfeb height 8 > select clear > select #1/A:681 4 atoms, 3 bonds, 1 residue, 1 model selected > label sel residues text DUF283 color #969687 height 8 > select #1/A:720 7 atoms, 6 bonds, 1 residue, 1 model selected > label sel residues text D-Linker color #58588e height 8 > save "D:/Promotion/002_Material/Proteine, > PDB/ChimeraX/hDicer_ChimeraX/hDicer_5zak_viridis_categorical_named.cxs" > select #1/A:842 8 atoms, 7 bonds, 1 residue, 1 model selected > label sel residues text Platform color #cbcb4a height 8 > select #1/A:917 9 atoms, 8 bonds, 1 residue, 1 model selected > label sel residues text PAZ color #7f7f90 height 8 > select #1/A:1072 5 atoms, 4 bonds, 1 residue, 1 model selected > label sel residues text Connector color #bcbc5f height 8 > select #1/A:1072 5 atoms, 4 bonds, 1 residue, 1 model selected > label sel residues text Connector color #bcbc5f height 0 > select #1/A:1065 8 atoms, 7 bonds, 1 residue, 1 model selected > label sel residues text Connector color #bcbc5f height 8 > select #1/A:1288 11 atoms, 10 bonds, 1 residue, 1 model selected > label sel residues text C-Linker color #737391 height 8 > select #1/A:1592 7 atoms, 7 bonds, 1 residue, 1 model selected > label sel residues text RNaseIIIA color #aeae70 height 8 > select #1/A:1840 7 atoms, 7 bonds, 1 residue, 1 model selected > label sel residues text RNaseIIIB color #3a3a5f height 8 > select #1/A:1886 4 atoms, 3 bonds, 1 residue, 1 model selected > label sel residues text dsRBD color #e73952 height 8 > save "D:/Promotion/002_Material/Proteine, > PDB/ChimeraX/hDicer_ChimeraX/hDicer_5zak_viridis_categorical_named.cxs" ——— End of log from Wed Jan 31 14:53:35 2024 ——— opened ChimeraX session BLAST job failed > silhouette Unknown command: silhouette > silhouette @:A Unknown command: silhouette @:A > silhouette #A Unknown command: silhouette #A > save "D:/Promotion/002_Material/Proteine, > PDB/ChimeraX/hDicer_ChimeraX/hDicer_5zak_viridis_categorical_named_test.cxs" > open "D:\Promotion\002_Material\Proteine, > PDB\ChimeraX\hDicer_ChimeraX\hDicer_5zak_viridis_categorical_named_test.cxs" > format session Unable to restore session, resetting. Traceback (most recent call last): File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 713, in restore self.reset() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 552, in reset sm.reset_state(container, self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 641, in reset_state task.terminate() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 208, in terminate self.session.tasks.remove(self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 556, in remove self.__delitem__(task.id) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 545, in __delitem__ task = self._tasks[key] ~~~~~~~~~~~^^^^^ KeyError: 1 Traceback (most recent call last): File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 713, in restore self.reset() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 552, in reset sm.reset_state(container, self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 641, in reset_state task.terminate() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 208, in terminate self.session.tasks.remove(self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 556, in remove self.__delitem__(task.id) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 545, in __delitem__ task = self._tasks[key] ~~~~~~~~~~~^^^^^ KeyError: 1 During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest self._callback(info) File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept return interceptor(request_info, *args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept chimerax_intercept(*args, view=view, session=session) File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py", line 375, in thread_safe func(*args, **kw) File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 446, in defer cxcmd(session, topic) File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd run(session, cmd) File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 213, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 514, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\core_formats\\__init__.py", line 37, in open return cxs_open(session, data, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 1017, in open session.restore(stream, path=path, resize_window=resize_window, combine=combine) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 755, in restore self.reset() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 552, in reset sm.reset_state(container, self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 641, in reset_state task.terminate() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 208, in terminate self.session.tasks.remove(self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 556, in remove self.__delitem__(task.id) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 545, in __delitem__ task = self._tasks[key] ~~~~~~~~~~~^^^^^ KeyError: 1 KeyError: 1 File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 545, in __delitem__ task = self._tasks[key] ~~~~~~~~~~~^^^^^ See log for complete Python traceback. > open "D:\Promotion\002_Material\Proteine, > PDB\ChimeraX\hDicer_ChimeraX\hDicer_5zak_viridis_categorical_named_test.cxs" > format session Unable to restore session, resetting. Traceback (most recent call last): File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 713, in restore self.reset() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 552, in reset sm.reset_state(container, self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 641, in reset_state task.terminate() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 208, in terminate self.session.tasks.remove(self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 556, in remove self.__delitem__(task.id) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 545, in __delitem__ task = self._tasks[key] ~~~~~~~~~~~^^^^^ KeyError: 1 Traceback (most recent call last): File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 713, in restore self.reset() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 552, in reset sm.reset_state(container, self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 641, in reset_state task.terminate() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 208, in terminate self.session.tasks.remove(self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 556, in remove self.__delitem__(task.id) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 545, in __delitem__ task = self._tasks[key] ~~~~~~~~~~~^^^^^ KeyError: 1 During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest self._callback(info) File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept return interceptor(request_info, *args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept chimerax_intercept(*args, view=view, session=session) File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py", line 375, in thread_safe func(*args, **kw) File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 446, in defer cxcmd(session, topic) File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd run(session, cmd) File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 213, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 514, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\core_formats\\__init__.py", line 37, in open return cxs_open(session, data, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 1017, in open session.restore(stream, path=path, resize_window=resize_window, combine=combine) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 755, in restore self.reset() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 552, in reset sm.reset_state(container, self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 641, in reset_state task.terminate() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 208, in terminate self.session.tasks.remove(self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 556, in remove self.__delitem__(task.id) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 545, in __delitem__ task = self._tasks[key] ~~~~~~~~~~~^^^^^ KeyError: 1 KeyError: 1 File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 545, in __delitem__ task = self._tasks[key] ~~~~~~~~~~~^^^^^ See log for complete Python traceback. > open "D:\Promotion\002_Material\Proteine, > PDB\ChimeraX\hDicer_ChimeraX\hDicer_5zak_viridis_categorical_named_test.cxs" > format session Unable to restore session, resetting. Traceback (most recent call last): File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 713, in restore self.reset() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 552, in reset sm.reset_state(container, self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 641, in reset_state task.terminate() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 208, in terminate self.session.tasks.remove(self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 556, in remove self.__delitem__(task.id) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 545, in __delitem__ task = self._tasks[key] ~~~~~~~~~~~^^^^^ KeyError: 1 Traceback (most recent call last): File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 713, in restore self.reset() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 552, in reset sm.reset_state(container, self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 641, in reset_state task.terminate() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 208, in terminate self.session.tasks.remove(self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 556, in remove self.__delitem__(task.id) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 545, in __delitem__ task = self._tasks[key] ~~~~~~~~~~~^^^^^ KeyError: 1 During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest self._callback(info) File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept return interceptor(request_info, *args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept chimerax_intercept(*args, view=view, session=session) File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py", line 375, in thread_safe func(*args, **kw) File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 446, in defer cxcmd(session, topic) File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd run(session, cmd) File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 213, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 514, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site- packages\chimerax\core_formats\\__init__.py", line 37, in open return cxs_open(session, data, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 1017, in open session.restore(stream, path=path, resize_window=resize_window, combine=combine) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 755, in restore self.reset() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 552, in reset sm.reset_state(container, self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 641, in reset_state task.terminate() File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 208, in terminate self.session.tasks.remove(self) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 556, in remove self.__delitem__(task.id) File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 545, in __delitem__ task = self._tasks[key] ~~~~~~~~~~~^^^^^ KeyError: 1 KeyError: 1 File "C:\Python32\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py", line 545, in __delitem__ task = self._tasks[key] ~~~~~~~~~~~^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 - Build 25.20.100.6793 OpenGL renderer: Intel(R) UHD Graphics 630 OpenGL vendor: Intel Python: 3.11.2 Locale: de_DE.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: HP Model: HP EliteDesk 800 G5 TWR OS: Microsoft Windows 10 Education (Build 19045) Memory: 34,123,063,296 MaxProcessMemory: 137,438,953,344 CPU: 6 Intel(R) Core(TM) i5-9500 CPU @ 3.00GHz OSLanguage: de-DE Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 comtypes: 1.1.14 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 23.2 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pywin32: 305 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 WMI: 1.5.1
Change History (2)
comment:1 by , 21 months ago
Component: | Unassigned → Sessions |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → KeyError restoring tasks |
comment:2 by , 18 months ago
Resolution: | → fixed |
---|---|
Status: | assigned → closed |
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